text - https://howfarawayisit.com/wp-content/uploads/2025/08/The-Chemistry-of-Life.doc music free version - For life to have formed on Earth, the starting mix of available atoms would have to combine into simple molecules [like methane, ethane and ethene]. Simple molecules would have to combine into more complex molecules [like carbon chains with chemical groups like carboxyl and phosphate groups]. Then these smaller complex molecules would have to combine into even more complex monomer molecules [like acids found in proteins: asparagine, glycine, tyrosine and alanine. And bases found in DNA: guanine, adenine, cytosine, and thymine]. Then these complex molecules would have to combine into to macro-molecules of life.
Music: - Mozart; Adagio (from Clarinet Concerto) from the album Meditation: Classical Relaxation, 2010
The making and breaking of a chemical
bond leading to changes in the
composition of the matter is called a
chemical reaction. Here's an example. We
have two hydrogen molecules and one
oxygen molecule as the reactants.
The chemical reaction breaks the
covealent bonds of both the hydrogen and
oxygen molecules and reorganizes the
atoms. The product of the chemical
reaction is two molecules of water.
It's an exothermic reaction when energy
is released. It's an endothermic
reaction when energy is absorbed.
Here we see that the energy absorbed to
break the reactants bonds is less than
the amount of energy released when the
products bonds are formed. So this one
is an exothermic chemical reaction.
Here's a chemical reaction that ionizes
water via a process called dissociation.
It is very important in the chemistry of
life.
Occasionally, a hydrogen atoms proton
participating in a hydrogen bond between
two water molecules dissociates from one
of the water molecules and associates
with the other. Dissociation involves
breaking the covealent bond with the
shared hydrogen electron remaining in
the valence shell of the oxygen atom and
the proton forming a covealent bond with
the other oxygen atom.
The receiving molecule is called a
hydronium ion. It has an extra positive
charge having received the positively
charged proton. It is referred to as a
hydrogen ion. The other molecule is
called a hydroxide ion. it has a
negative charge.
This reaction works the other way as
well where the hydrononeium ion loses
the proton back to a hydroxide ion.
These ions are very reactive. They
participate in ionic covealent and
hydrogen bonds with a wide variety of
other molecules.
Because it works both ways and
equilibrium is established in any given
volume of water. There are approximately
33.4 4 trillion trillion water molecules
in one liter of pure water. Only one
water molecule out of every 554 million
is dissociated.
Yet this small percentage for ions gives
us 60,000 trillion of them in a liter.
In pure water, the concentration of
hydroxide ions and hydrononeium ions are
each 10us 7. Although the concentrations
of hydroxide and hydrronium are equal in
pure water, the presence of other
substances can change that.
A substance that increases the number of
hydrogen ions in a solution is called an
acid.
Hydrochloric acid is a good example. It
loses its hydrogen atom to a water
molecule, adding an additional hydrogen
ion to the solution.
A substance that decreases the number of
hydrogen ions in a solution is called a
base. Ammonia is a good example. It
takes a hydrogen ion out of the
solution.
The relative abundance of hydroxide ions
defines pH values and has a dramatic
influence on how molecules behave in a
watery solution, including the inside of
a living cell. In fact, the internal pH
of most living cells must remain close
to 7.2. 2, including the synthetic
living cell JCVI,
synthesis 3A.
We'll study this cell a bit later.
